Exam 2 Flashcards
What is energy?
The capacity to do work or supply heat
What is potential energy?
Stored energy
What is kinetic energy?
Active motion
What does the first law of thermodynamics state?
- Energy is conserved
- It cannot be created or destroyed
- It can be transferred or transformed
What kind of energy is thermal energy?
Kinetic
What kind of energy is potential?
Chemical
What is enthalpy?
The total energy of a molecule (the sum of potential and kinetic energy)
What is potential energy in molecules related to?
The structural arrangement of atoms or molecules
Is potential energy high or low in strong bonds?
low
Is potential energy high or low in weak bonds?
high
Breaking a strong bond ______ energy.
requires
Creating a strong bond ______ energy.
produces
Breaking a weak bond _______ energy.
produces
Creating a weak bond _____ energy.
requires
C-C and C-H have high _______ energy bonds.
potential
What is kinetic energy in relation to molecules?
molecular movement
What is kinetic energy in molecules measured as?
Temperature
What is entropy?
The amount of disorder in a group of molecules (S)
What is the second law of thermodynamics?
Total entropy increases in isolated systems
When does chemical equilibrium occur?
When the forward and reverse reactions proceed at the same time, and when the quantities of reactants and products remain constant.
When are chemical reactions spontaneous?
When they proceed without any continuous external influence, no energy is added.
Spontaneous reactions can be very ____ or very ____.
fast, slow
What does a non-spontaneous reaction rely on?
External influence (needs energy)
What does the spontaneity of a reaction depend on?
The change in potential energy (delta H) and the degree of order (delta S)
Products often have ______ potential energy than the reactants.
less
Products are _____ ordered than the reactants.
less
What are qualities of reactants?
High potential energy, more order (lower entropy)
What are qualities of products?
Low potential energy, less order (higher entropy)
What is delta H?
The change in potential energy
What is the formula for delta G?
delta G= delta H - T(delta S)
What is delta S?
Difference in entropy
What is T?
Temperature
What does delta G<0 mean?
Exergonic (spontaneous) reaction
What does delta G>0 mean?
Endergonic (non-spontaneous) reaction
What does energetic coupling do?
Allows chemical energy to be released from one reaction to drive another. Exergonic reaction allows for endergonic reaction to occur. Occurs through the hydrolysis of ATP
What type of reaction is the condensation of nucleoside monophosphates?
Endergonic (does not occur in nature), which is why ATP has triphosphates
What type of reaction is the condensation of nucleoside triphosphates?
Exergonic
What type of reaction is the synthesis of starch?
Exergonic (order is created but new molecules have stronger bonds)
What are enzymes?
A class of proteins that speed up chemical reactions
Why do all modern life forms require enzymes?
Most chemical reactions are very slow
What are the requirements for a chemical reaction to occur?
Reactants must collide in a precise orientation, the free energy of the transitional state should not be too high
How do enzymes work?
Enzymes bring substrates (reactants) together in specific positions that facilitate reactions. Substrates bind to the enzyme’s active site. Interactions between the enzyme and substrate stabilize the transition state, and lower the activation energy required for the reaction to proceed.
What is the transitional state?
The fleeting molecular configuration when old chemical bonds are breaking and new ones are building
Enzymes are _______.
catalysts
How are enzymes catalysts?
They lower the activation energy of a reaction by lowering the free energy of the transition state, they do not change delta G, and they are not consumed in the reaction
What are the steps of Enzyme Catalysis? describe them
- Initiation- reactants bind to the active site in a specific orientation, forming an enzyme-substrate complex.
- Transition state facilitation- Interactions between enzyme and substrate lower the activation energy required
- Termination- Products have lower affinity for active site and are released. Enzyme is unchanged
How does the speed of an enzyme-catalyzed reaction change with different substrate concentrations?
- Increases linearly at low substrate concentrations
- Slows as substrate concentration increases
- Reaches maximum speed at high substrate concentrations
What limits the rate of catalysis?
Enzymes can be saturated. The rate of a reaction is limited by the amounts of substrates present and enzymes available. Active sites cannot accept substrates any faster no matter how large the concentration of substrates gets.
How do physical conditions affect enzyme function?
Enzymes are proteins and have specific foldings. Enzymes function best at some particular temperature and pH. Temperature and pH affects the enzyme’s shape and reactivity.
What does the rate of enzyme-catalyzed reactions depend on? (6 things)
- substrate concentration
- enzyme concentration
- temperature
- pH
- the enzyme’s intrinsic affinity for the substrate
- enzyme regulation (competitive inhibition, allosteric regulation, enzyme phosphorylation)
The function of enzymes needs to be ______. They need to be _____ ___ and ______ __ at specific times.
regulated, turned off, turned on
What is enzyme regulation via non-covalent interactions?
Regulators do not form covalent bonds with the enzyme. Competitive inhibition and allosteric regulation (allosteric activation, allosteric inhibition)
What is competitive inhibition?
The substrates cannot bind when a regulatory molecule binds to the enzyme’s activation site
What is allosteric regulation?
The regulatory molecules do not bind to the active site, but bind in another place. This changes the shape of the molecule.
What is allosteric activation?
The active sites becomes available to the substrates when a regulatory molecule binds to a different site on the enzyme.
What is allosteric inhibition?
The active site becomes unavailable to the substrates when a regulatory molecule binds to a different site on the enzyme
What is enzyme regulation via covalent bonds?
The function of an enzyme can be altered by a chemical change in its primary structure. Phosphorylation of an enzyme.
What are the most common modifications of enzymes via covalent interactions?
The addition of one or more phosphate groups to Ser, Thr, Tyr, and His
What is phosphorylation of an enzyme?
A reversible modification to the protein’s structure with the addition of phosphate groups.
What is metabolism?
Chemical reactions that occur in a cell
Enzymes work together in _________ pathways.
metabolic
What is a metabolic pathway?
A series of reactions, each catalyzed by a different enzyme to build biological molecules.
What metabolic pathways produce ATP?
Cellular respiration and fermentation
What is cellular respiration?
A set of reactions that produces ATP using an electron
What is aerobic respiration?
The electron acceptor is oxygen. Very common and the most efficient way to produce ATP
What is anaerobic respiration?
Electron acceptor is not oxygen. Occurs only in selected prokaryotes
What is fermentation?
A set of reactions that produces ATP without oxygen and an electron transport chain ( very common as cells are often limited by oxygen availability, inefficient way to produce ATP)
How long does ATP last in cells?
30 seconds to a couple minutes
Why must cells produce ATP constantly?
ATP is unstable and cannot be stored
What does the hydrolysis of ATP often result in?
The transfer of the released phosphate group to a different molecule and formation of high potential energy bonds
How much ATP goes towards protein synthesis, membrane pumps, RNA/DNA synthesis, and other metabolic reactions?
- Protein synthesis: 33%
- Membrane pumps: 33%
- RNA/DNA synthesis: 25%
- Other metabolic reactions: 9%
How is glucose oxidized?
Through a series of carefully controlled redox reactions. Carbon atoms of glucose are oxidized to form carbon dioxide. Oxygen is reduced and forms water. The resulting change in Gibbs free energy is used to synthesize ATP from ADP and Pi
What is a redox reaction?
An electron is transferred from one molecule to another. A reduced molecule gains electrons and an oxidized molecule losses electrons. Electrons can be transferred completely or shift positions in their covalent bonds.
During respiration, carbon is ______ and oxygen in ______.
oxidized, reduced
What happens when an electron is transferred from one molecule to another in a redox reaction?
It is usually accompanied by a proton (H+). A reduced molecule gains a proton and an oxidized molecule losses a proton.
A reduction often adds ________ atoms and an oxidation often removes _________ atoms.
hydrogen x2
Why are NADH and FADH2 important molecules for cellular respiration?
They readily donate electrons to other molecules. They have reducing power and are called electron carriers. They have a lot of potential energy
What is the energy flow during respiration?
Glucose ——-> NADH and FADH2 ——–> ATP
What are the four steps of cellular respiration?
- glycolysis
- pyruvate processing
- citric acid cycle
- electron transport and chemiosmosis
Does glycolysis use or create O2?
no
What is glycolysis?
A series of 10 chemical reactions (requires 10 enzymes). Glucose is broken down into two molecules of pyruvate (carbon in pyruvate is more oxidized compared to glucose), and the potential energy released is used to make 2 ATP and 2 NADH
Where does glycolysis occur?
In the cytosol of the cell
What phases does glycolysis consist of?
An energy investment phase and an energy payoff stage
How many reactions are in the energy investment phase? The energy payoff phase?
3, 7
What happens in the energy investment phase?
2 molecules of ATP are consumed and glucose is phosphorylated twice
Once the energy investment phase is completed, have any redox reactions occurred?
no
What happens during the energy payoff phase?
Sugar is split to form two pyruvate molecules , 2 molecules of NAD+ are reduced to NADH, and 4 molecules of ATP are formed by substrate-level phosphorylation (net gain of 2 ATP)
When and where does substrate level phosphorylation occur?
It occurs when ATP is produced by the enzyme-catalyzed transfer of a phosphate group from an intermediate substrate to ADP. It occurs in glycolysis (reactions #7 and #10)
When does glycolysis occur and what does the speed of it depend on?
It occurs when the cell needs ATP. The speed of it depends on the need for ATP.
What is glycolysis regulated by?
Feedback inhibition
What is feedback inhibition?
When an enzyme in a pathway is inhibited by the product of that pathway.
When ATP is abundant in cells, glycolysis _______.
stops
How does feedback inhibition help cells when ATP is scarce?
It helps conserve glucose stores
How is the enzyme that catalyzes reaction #3 of glycolysis inhibited by ATP?
allosterically
What do high levels of ATP inhibit during glycolysis?
The enzyme phosphofructokinase that catalyzes reaction #3
What is the affinity of the active site of phosphofructokinase and what does it mean?
High affinity, will bind ATP at low concentrations
What is the affinity of the regulatory site of phosphofructokinase and what does it mean?
Low affinity, will bind ATP only when it is very abundant
What do high ATP concentrations cause?
ATP to bind to the regulatory site, changing the enzyme’s shape, drastically decreasing the reaction rate at the active site.
During glycolysis, when each molecule of glucose is catabolized to two molecules of pyruvate, ______________________________________________.
most of the potential energy contained in glucose is retained in the two pyruvates
What steps of cellular respiration occur in the mitochondria in eukaryotes?
2-4
What happens to the pyruvates produced during glycolysis?
They are transported from the cytosol into the mitochondria by channels into the matrix.
What happens during pyruvate processing?
The pyruvate is catalyzed by the enzyme pyruvate dehydrogenase. During these reactions, another molecule of NADH is synthesized and one of the carbon atoms in pyruvate is oxidized to CO2. Acetyl CoA is produced
What is coenzyme A?
A substrate
What is the Krebs Cycle?
A series of 8 reactions. The oxidation and recycling of carboxylic acids.
How is citrate formed in the beginning of the Krebs cycle?
It is formed form Acetyl CoA and oxaloacetate
What is the first molecule in the Krebs cycle? What is the last?
citrate, oxaloacetate
What is the substrate of the Krebs cycle? What are the products?
Substrate- acetyl CoA
Products- 2CO2, 3NADH, FADH, GTP
What happen to the Krebs Cycle when energy supplies are high?
It slows down
The cycle can be _____ ___ at multiple points.
turned off
What is reaction #1 of the Krebs cycle regulated by?
ATP
What are reaction #3 and #4 regulated by in the Krebs cycle?
Feedback inhibition via NADH and ATP
What do steps 1-3 of the Krebs cycle do?
Oxidation of carbon atoms
What is the potential energy of C-H bonds gradually converted into the energy of during the Krebs cycle?
NADH, FADH2, and ATP (GTP)
How are ATP and GTP formed?
Substrate Phosphorylation
What happens during the 4th step of respiration (electron transport and oxidative phosphorylation)?
NADH and FADH2 are oxidized in reactions leading to ATP production
What are the products of glycolysis?
2 pyruvates, +2ATP, +2NADH
What are the products of pyruvate processing?
2 Acetyl CoA, +2NADH
What are the products of the Krebs cycle?
4CO2, 6NADH, 2FADH2, 2GTP (or 2ATP)
What is the electron transport chain (ETC)?
The extraction of energy from high-energy molecules (10NADH and 2FADH2) formed during glycolysis, pyruvate processing, and the citric acid cycle.
What are most ETC molecules?
Proteins containing chemical groups that facilitate redox reaction
How many of the ETC proteins are embedded in the inner mitochondrial membrane?
All but one
What is the first “step” of electron transport?
NADH donated electrons to protein complex I.
What type of reaction is it when NADH donates electrons to protein complex I? What happens during this step?
Redox reaction. Complex I is a proton pump, meaning it can move protons into the intermembrane space against the electrochemical gradient (the energy comes from the redox reaction). NAD+ is a byproduct, formed in the matrix.
What is the second “step” of the ETC chain?
FADH2 donates electrons to protein complex II
What type of reaction is it when FADH2 donates electrons to protein complex II? What happens during this step?
Redox reaction. Complex II is not a proton pump, so protons are not moved against their electrochemical gradients. FADH is a byproduct, formed in the matrix.
What is “Q” in the ETC?
Ubiquinone, which is a lipid instead of a protein
What do complexes I and II transfer electrons to?
Ubiquinone (Q)
What can Q easily do?
move throughout the membrane
What does Q do?
Transfers electrons to complex II and transfers H+ to the intermembrane space.
What are cytochromes?
Proteins containing a heme group
What does cytochrome c do?
Transfer electrons between complexes III and IV
What is the function of complex IV in the ETC?
To transfer electrons to oxygen and to pump H+ from the matrix to intermembrane space
What is oxygen during the ETC?
an electron acceptor
What is water during the ETC?
a by-product
The energy released as _____ move through the ETC is used to pump ______ into the intermembrane space (inside of cristae).
electrons, protons
(forms a strong electrochemical gradient)
Gradient of ions is a form of _______ energy.
potential
What does the ETC ultimately do?
Creates a proton gradient
What is the proton gradient established by the ETC used for?
to synthesize ATP (chemiosmosis)
What is ATP synthase?
A membrane-bound, proton-transporting base
What does the flow of protons do to ATP synthase?
Spins the rotor, which catalyzes the phosphorylation of ADP to ATP
How much ATP does oxidative phosphorylation produce?
25 ATP
How much ATP and GTP does substrate-level phosphorylation produce?
2 ATP and 2 GTP
What is the primary substrate for cellular respiration?
glucose
The hydrolysis of what can also be used for cellular respiration?
Sugars, fats, and proteins
In prokaryotes, where do the different stages of cellular respiration occur?
Glycolysis, pyruvate processing, and the citric acid cycle occur in the cytosol. Electron transport and oxidative phosphorylation occur in the mesosome.
What organisms use anaerobic respiration?
Some prokaryotes living in oxygen-poor environments
Why is oxygen the most effective electron acceptor?
It is highly electronegative. There is also a large difference between the potential energy of NADH and O2 electrons, which allows for the generation of a large proton-motive force. This allows for ATP production.
What is fermentation?
The production of ATP without ETC
What is a limiting factor for glycolysis in the absence of oxygen?
NAD+
What are the two ways to regenerate NAD+?
Lactic fermentation and ethanol fermentation
What is produced by lactic fermentation?
2ATP, 2 NAD+, and 2 lactate
What is produced by ethanol fermentation?
2 ATP, 2 NAD+, 2 CO2, and 2 ethanol
Fermentation is extremely ___________.
Inefficient
What is the most important process on Earth?
Photosynthesis
What does photosynthesis use light to create?
ATP and NADPH
What are ATP and NADPH used for in photosynthesis?
To reduce CO2 to sugar
In photosynthesis, carbon is __________ and oxygen ________.
reduced, oxidized
What is the basic reaction of photosynthesis?
6 CO2 + 6 H20 + energy ———> (CH20)4H (glucose) + 6 O2
What are the two sets of reactions that occur during photosynthesis?
Light-capturing reactions and Calvin cycle reactions
What do light-capturing reactions produce from what?
ATP and NADPH from O2 and H2O
What do Calvin cycle reactions produce from what?
Sugar from CO2
Light acts as both a ________ and as a ____.
particle, wave
What is light as a particle?
Photon
What is light characterized by as a wave?
Its wavelength
What type of light is both highly energetic and mainly what the sun produces?
Visible light
Which has more energy: shorter or longer wavelengths?
Shorter
What are pigments?
Molecules that absorb visible light
What are the two major classes of pigments in plants leaves?
Chlorophylls and Carotenoids
What is one method in which pigments can be isolated?
Thin layer chromatography
What pigments are most effective at triggering photosynthesis?
Pigments that absorb violet-blue and red wavelengths
What are some characteristics of chlorophylls?
A “head” and a long “tail”
What does the “tail” of chlorophylls consist of?
Isoprene subunits
What does the “head” of chlorophylls consist of?
A large ring structure with a magnesium atom in the middle
What are carotenoids?
Accessory pigments that absorb light
What do carotenoids do?
They pass the energy on to chlorophyll and extend the range of wavelengths that can drive photosynthesis.
What is a photosystem?
When chlorophyll and carotenoid molecules work together with proteins in groups and form a complex.
What are the two major elements of photosystems?
An antenna and a reaction center
What happens when a red or blue photon strikes a pigments molecule in the antenna complex?
The energy is absorbed and en electron is excited
How is energy transferred inside the antenna complex of a photosystem?
From one molecule to the next until it reaches the reaction center
What happens after energy is transferred to the reaction center of a photosytem?
Excited electrons are transferred from a chlorophyll to a specialized molecule (electron acceptor) and into an ETC
Photosystems are part of ___ in chloroplasts.
ETC
What happens within the ETC of chloroplasts?
Light is absorbed, electrons are transferred and an H+ gradient is established, and synthesis of NADPH and ATP.
How does Photosystem I work?
- Pigments in the antenna complex absorb photons and pass the energy to the reaction center
- Excited electrons from one reaction center are passed to ferredoxin, then to NADP+ reductase
What is the goal of photosystem I?
To create NADPH
Where does Photosystem I replace its electron from once it loses it?
PC (plastocyanin)
How does Photosystem II work?
- Pigments in the antenna complex absorb protons and pass the energy to the reaction center
- Excited electrons from the reaction center are pass to PQ (plastoquinone) and then to the cytochrome complex
What is the goal of photosystem II?
To create an H+ gradient
What is the energy transfer of photosystem I?
Light ——> electron movement ——> NADPH
What is the energy transfer of photosystem II?
Light —–> electron movement —–> H+ gradient
How does Photosystem II obtain electrons?
When excited electrons leave photosystem II and enter the ETC, the photosystem becomes electronegative. This allows enzymes to remove electrons from water, leaving protons and oxygen.
Why does photosystem II oxidize water?
To replace electrons used during light reactions
What is oxygenic photosynthesis?
When photosystem II “splits” water.
What is the formula for oxygenic photosynthesis?
2 H2O ——> 4 H+ + 4 e- + O2
Oxygen was almost nonexistent on Earth before what?
Before enzymes evolved that could catalyze the oxidation of water
The oxygen released from ________ ______________ was critical to the evolution of life as we know it.
Oxygenic photosynthesis
Why does movement of electrons in ETC occur?
Because of differences in electronegativity of its components
What happens to a molecule’s electronegativity once it obtains an electron?
It goes down
What is chemiosmosis (Photophosphorylation)?
When the flow of protons through ATP synthases causes a change in its shape, driving the phosphorylation of ADP.
Which photosystem drives the synthesis of ATP?
Photosystem II
Which photosystem yields reducing power in the form of NADPH?
Photosystem I
Which photosynthetic organisms make up most of the world’s oxygen?
Marine
Where do light capturing reactions occur?
In the thylakoid membrane
Where do Calvin cycle reactions occur?
In the stoma
What are the three phases of the Calvin cycle?
- Fixation
- Reduction
- Regeneration
What happens during the fixation phase of the Calvin Cycle?
CO2 reacts with ribulose bisphosphate (RuBP) and produces two 3-phosphoglycerate (PGA) molecules.
What is carbon fixation?
The attachment of CO2 to an organic compound
What is the formula of the fixation phase of the Calvin Cycle?
C5 + CO2 ——> 2 C3
What happens during the reduction phase of the Calvin Cycle?
The PGA molecules are phosphorylated by ATP and reduced by NADPH. This produces G3P (glyceraldehyde 3-phosphate)
What does the reduction phase of the Calvin Cycle use?
ATP and NADPH produced by light dependent reactions
Why does the reduction phase of the Calvin Cycle use ATP?
ATP activates molecules which leads to formation of high potential energy bonds. It is also used for energetic coupling
What type of reaction is the reduction phase of the Calvin Cycle?
Exergonic
The Calvin Cycle must occur when _____ is available.
light
What happens to some G3P of the Calvin Cycle?
It leaves for biosynthesis of glucose and fructose, which later is used to make sucrose.
What happens during the regeneration phase of the Calvin Cycle?
The remaining G3P is used in reactions that regenerate RuBP (requires ATP)
All reactions in the Calvin Cycle are catalyzed by _______.
enzymes
Carbon is ________ in the Calvin Cycle.
reduced
Carbon is _______ in the Krebs Cycle.
oxidized
What is the importance of rubisco?
The CO2-fixing enzyme. It is found in all photosynthetic organisms and thought to be the most abundant enzyme on Earth.
Rubisco is not an _________ enzyme.
efficient
What is the good reaction of rubisco?
When it is a carboxylase.
C5 + CO2 —–> 2 C3
What is the bad reaction of rubisco?
When it is an oxygenase.
C5 + O2 ——-> C3 + C2
____ and ____ compete at rubisco’s active site.
O2 and CO2
What is photorespiration?
When O2 and RuBP react in rubisco’s active site
What does photorespiration do?
Undoes photosynthesis. It consumes energy (ATP) and releases CO2
When does rubisco favor carbon fixation over photorespiration?
When CO2 concentration is high and O2 concentration is low
What does the concentration of CO2 and O2 in plant tissues depend on?
Stomata
What do stomata consist of?
Two guard cells that change shape to open or close.
What happens during the day with stomata?
Stomata open to allow atmospheric CO2 to diffuse into the leaf, at the same time water and O2 diffuse out.
Stomata are ____ during the day and _____ closed at night.
open, closed
What does closing the stomata stop?
CO2 delivery and the Calvin Cycle (increases photorespiration)
How do plants in hot, dry climates prevent photorespiration?
They increase concentration of CO2 and decrease the concentration of O2 in the vicinity of rubisco.
What plants are capable of isolating rubisco from O2?
C4 and CAM
C4 photosynthesis and CAM function as ___ _____.
CO2 pumps
What are the chemical reactions of C4 and CAM photosynthesis?
CO2 + C3 —> C4; C4 is moved to a place with rubisco and low O2; C4 —–> CO2 + C3 (C4 is broken); CO2 is used for the Calvin Cycle
Cyanobacteria along with all photosynthetic plants perform _________ and _____ _________.
photosynthesis, cellular respiration
